Oct-1 is a transcription factor belonging to the POU family (Clerc et al.

1988) (Herr et al. 1988) (Ryan and Rosenfeld 1997). The members of this family

are involved in a broad range of biological processes like transcription of

housekeeping genes (Oct-1), pluripotency of embryonic stem cells (Oct-4) or

development of immune system (Oct-1, Oct-2) (Spaniol et al. 1996). The

transcription factor Oct-1 is ubiquitously expressed in embryonic and adult

tissues, and regulates the expression of a variety of genes. Previous studies

described Oct-1 to be regulated at the protein level by phosphorylation in a cell

cycle dependent manner. In addition, more recently it has been shown that Oct-

1 is induced in response to DNA damage and modulates the activity of genes

like GADD45 important for the cellular stress response (Segil et al. 1991) (Zhao

et al. 2000) (Jin et al. 2001) (Fan et al. 2002) (Tantin et al. 2005)..

Knockout and a conditional oct-1 knockout alleles were created in our laboratory,

and used to generate Oct-1 deficient mouse embryonic fibroblast (MEFs) and

embryonic stem cells (ES). We used them as a model to study the cellular

response to stress in absence of Oct-1. We have found that cells lacking Oct-1

were less sensitive to stress lik

Bles W.

Groen E.L.

Howard I.P.

Telford L.

Warren W.H.

English

Ksander de Winkel

Bruno Jorge Correia Grácio

Eric Groen

Peter Werkhoven

Crossref

Visual Inertial Coherence Zone in the Perception of Heading

Knowledge of human motion perception can be applied in the optimization of motion cueing algorithms. In the past it has been shown that some discrepancies between the amplitude or phase of a visual and inertial cue go unnoticed. These acceptable discrepancies are referred to as coherence zones. In the present experiment we investigate whether a coherence zone applies to the direction of visual and inertial motion cues. More specifically, we investigated how much heading of an inertial stimulus may deviate from a visual stimulus suggesting ‘straight ahead’ motion, before the ‘straight ahead’ percept falls apart. Subjects were presented with congruent visual-inertial linear horizontal motion stimuli with varying heading and incongruent visual-inertial linear horizontal motion stimuli, in which a visual cue suggesting straight ahead motion was coupled with an inertial heading cue with varying heading. Subjects judged I) whether or not they moved straight ahead, and II) whether or not the visual and inertial stimulus were congruent. We fitted psychometric curves to the combined judgments and calculated detection thresholds for a violation of either criterion. The results show that the 50% detection thresholds are larger in the incongruent than in the congruent condition. We interpret the threshold for the incongruent condition as the size of the coherence zone. In conclusion: we provide evidence of a coherence zone for heading, as wella as a measure of the size of the heading coherence zone

de Winkel, K.

Correia Grácio, B.

Groen, E.

Werkhoven, P.

MPG.PuRe

Knowledge of human motion perception can be applied in the optimization of motion cueing algorithms. In the past it has been shown that some discrepancies between the amplitude or phase of a visual and inertial cue go unnoticed. These acceptable discrepancies are referred to as coherence zones. In the present experiment we investigate whether a coherence zone applies to the direction of visual and inertial motion cues. More specifically, we investigated how much heading of an inertial stimulus may deviate from a visual stimulus suggesting 'straight ahead' motion, before the 'straight ahead' percept falls apart. Subjects were presented with congruent visual-inertial linear horizontal motion stimuli with varying heading and incongruent visual-inertial linear horizontal motion stimuli, in which a visual cue suggesting straight ahead motion was coupled with an inertial heading cue with varying heading. Subjects judged I) whether or not they moved straight ahead, and II) whether or not the visual and inertial stimulus were congruent. We fitted psychometric curves to the combined judgments and calculated detection thresholds for a violation of either criterion. The results show that the 50% detection thresholds are larger in the incongruent than in the congruent condition. We interpret the threshold for the incongruent condition as the size of the coherence zone. In conclusion: we provide evidence of a coherence zone for heading, as wella as a measure of the size of the heading coherence zone

Winkel, K.N. de

Correia Grácio, B.J.

Groen, E.L.

Werkhoven, P.J.

NARCIS 

Visual-inertial coherence zone in the perception of heading

Dalvai, Mathieu

edoc

 1  The versatile transcription factor Oct-1:  A crucial protein in embryonic development and A key component of the stress cellular response.    Inauguraldissertation    zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät Der Universität Basel  Von  Mathieu Dalvai  Aus Strasbourg, (Frankreich)    Basel, 2008   2 Genehmigt von der Philosophisch-Naturwissenschftlichen Fakultät  auf Antrag von  Prof. Markus Affolter und Prof. Witold Filipowicz        Basel, den 24/04/2007 (datum der Fakultätssitzung)            Prof. Dr Hans Peter Hauri (Dekan)         3                    4                     5Acknowledgements    I would like to thank Pr. Patrick Matthias, my supervisor, who helped me a lot during this last four years by his theoretical and practical advices which allowed me to focus on what’s essential in science and also in life in general. Thanks also to the other thesis committee members, Pr. Markus Affolter and Pr. Witold Filipowicz. Thanks to Pr. Hans Schöeler and Fatima Cavaleri for their collaboration. At least, thanks to all facilities members who help me a lot.   The thesis is a long period with some pleasant times but also (sometimes….) with some difficult moments where you think that science is not for you and you could be a good shell-necklace seller in a pacific island….It’s during this black moment that your friends, your family, are there to help you in many ways. I would like to thank all of them, especially my parents, my brothers and my sisters in law, but foremost my wife Florence who I love very much and of course my little boy Gaël which was a great moral support.    Special thanks to my colleagues, for all the things that make work in the lab great fun, So-Hee, Camille, Chun, Gabi (women first) and also Teppei, Fabien, Alain, Markus and Oliver. Thanks also to all the former lab members Ralph, Boris, Yu and finally Alexander with whom I had a lot of serious and interesting discussions and drank some beers.   6                    7Contents  Summary of the thesis 17  1.    Introduction………………………………………………………..23     1.1    Cell cycle and regulation.………………………………………………………...23          1.1.1    Cell cycle phases……………………………………………………………...23          1.1.2    Cyclin-dependent kinase (CDK)……………………………………………..27          1.1.3    Cyclin dependent kinase inhibitor (CDKi)………………………………….. 31     1.2    p27 is a key negative regulator of G1/S checkpoint………………………...33     1.3    Cyclin D1, an important actor in G1/S transition……………………………. 37          1.3.1    Activation and activity of cyclin D1…………………………………………. 39     1.4    Receptor tyrosine kinase and signal transduction…………………………. 43          1.4.1    The RTK subclass 1: ERBB receptors……………………………………...45     1.5    The RAS/ERK signaling pathway……………………………………………….47          1.5.1    RAS/ERK signaling and cell cycle progression…………………………… 51     1.6    The PBK/AKT pathway……………………………………………………………53          1.6.1    PBK/AKT signaling: cell cycle progression and proliferation control…… 55     1.7    Cell cycle response to DNA damaging agent………………………………...57          1.7.1    p53 pathway…………………………………………………………………... 57          1.7.2     p21……………………………………………………………………………..61          1.7.3    BAX……………………………………………………………………………..63          1.7.4    GADD45………………………………………………………………………..65     1.8    The ubiquitous transcription factor Oct-1……………………………………. 69          1.8.1    Oct-1: cell cycle and stress cellular response…………………………...... 75   8                      9Chapter 1: Oct-1 is necessary for cell cycle arrest under stress                       Conditions……..…………………………...…………….79 2.    Results…………………………………………………………….. 81     2.1    Abstract…...………………………………………………………………………... 81     2.2    Introduction………………………………………………………………………... 83     2.3    Results……………………………………………………………………………….87     2.4    Additional data………..…………………………………………………………..123     2.5    Materials and Methods…………………………………………………………..127  Chapter 2: Oct-1 is an essential factor  in   embryogenesis   and              is  required  for  a  proper  extra-embryonic   tissues             formation………………..……………………………….135 1.    Introduction………………………………………………………137     1.1    Summary of mouse development……………………………………………..137     1.2    Gastrulation……………………………………………………………………….139     1.3    Cross-talks between extra-embryonic and embryonic tissues………….141     1.4    Transcription factors: ES pluripotency and trophectoderm differentiation.149     1.5    Primary data and objective of research projects…………………………..151 2.    Results……………………………………………………………153 3.    Discussion……………………………………………………….163 4.    Materials and methods………………………………………...169 References….…………………………………………………………175   10                    11Abbreviations   Aa:    amino acids BrdU:    bromodeoxyuridine CDC:    cell division cycle CDK:    cyclin dependent kinase CDKI:   cyclin dependent kinase inhibitor CFSE:   carboxyfluorescein diacetate succimidyl ester ChIP:    chromatin immunoprecipitation CRM1:   chromosome region maintenance DNA:    desoxyribonucleic acid EGF:    epidermal growth factor ERK:    extracellular-signal regulated kinase ES cells:   embryonic stem cells ExE:    extra-embryonic ectoderm F,f allele:   flox allele FACS:   fluorescence-activated cell sorting FGF:    fibroblast growth factor GADD45:   growth arrest DNA damage GDP:    guanosine diphosphate GTP:    guanosine triphosphate Gy:    gray H&E:    hematoxilin and eosin  ICM:    inner cell mass KO:    knock-out  12                          13MAPK:   mitogen activated protein kinase MEF:    mouse embryonic fibroblast NEBD:  nuclear envelope break-down  PCR:    polymerase chain reaction PGC:    primordial germ cells PKB:    protein kinase B Rb:    retinoblastoma RNA:    ribonucleic acid RT:    reverse transcriptase RTK:    receptor tyrosine kinase SH2:    sarcoma homology domain TE:   trophectoderm TGF-?:   transforming growth factor- ? TOR:    target of rapamycin TS cells:   trophoblastic stem cells UV:    ultraviolet Wt:    wild type        14                    15Summary of the thesis   Chapter 1   Oct-1 is a transcription factor belonging to the POU family (Clerc et al. 1988) (Herr et al. 1988) (Ryan and Rosenfeld 1997). The members of this family are involved in a broad range of biological processes like transcription of housekeeping genes (Oct-1), pluripotency of embryonic stem cells (Oct-4) or development of immune system (Oct-1, Oct-2) (Spaniol et al. 1996). The transcription factor Oct-1 is ubiquitously expressed in embryonic and adult tissues, and regulates the expression of a variety of genes. Previous studies described Oct-1 to be regulated at the protein level by phosphorylation in a cell cycle dependent manner. In addition, more recently it has been shown that Oct-1 is induced in response to DNA damage and modulates the activity of genes like GADD45 important for the cellular stress response  (Segil et al. 1991) (Zhao et al. 2000) (Jin et al. 2001) (Fan et al. 2002) (Tantin et al. 2005)..  Knockout and a conditional oct-1 knockout alleles were created in our laboratory, and used to generate Oct-1 deficient mouse embryonic fibroblast (MEFs) and embryonic stem cells (ES). We used them as a model to study the cellular response to stress in absence of Oct-1. We have found that cells lacking Oct-1 were less sensitive to stress like ?-irradiation, deprivation of glucose or amino acids but not to serum starvation or H2O2 treatment. Under glucose starvation, this effect is in part mediated by activation of the signalling protein ERK and PKB which leads to maintenance of the level of cyclin D1 protein in KO cells   16                          17comparable to the level without treatment in heterozygous or rescue cells. These proliferative signals allow to KO cells to bypass the G1 cell cycle checkpoint and to proliferate better. Under stress conditions like glucose starvation, Oct-1 regulates the cell cycle by blocking cells in G1 phase, and by controlling the expression of the cyclin dependent kinase inhibitor p27.  Chapter 1 of this thesis provides a general introduction about the regulation of cell cycle and, more particularly, about key proteins and important pathways of the progression and transition of G0/G1 and S phases. It also gives some background about pathways like PKB and ERK, or other signaling pathways like p53, which plays determinant roles in cellular responses after stress induction. The role of the transcription factor Oct-1 in cell cycle regulation in response to cellular stress is discussed in the results part.   Chapter 2   The POU transcription factors family was identified after the isolation of three mammalian transcription factors and a Caenorhabditis elegans developmental regulator: Pit-1, Oct-1, Oct-2 and Unc-86 (Ryan and Rosenfeld 1997). Oct-1 and Oct-2 proteins show a high degree of identity (90%) but differ in their expression pattern. Oct-1 is ubiquitously expressed, whereas Oct-2 is restricted to B cells, macrophages, hematopoietic cells, as well as cells of the central nervous system (Gerster et al. 1987) (He et al. 1989) (Staudt et al. 1988). Despite several studies, the exact role of Oct-1 and Oct-2 in immunoglobulin genes regulation and B-cell development is not well understood. In order to   18                         19investigate the functions of Oct-1 in B cells, our laboratory created a deficient mouse for Oct-1. Mice homozygous for oct-1 (-/-) were generated by crossing heterozygous +/- mice. Unfortunatly, these matings failed to produce any live born homozygous oct-1 -/- mutant, indicating that    Oct-1 is essential for embryonic mouse development.  In this second project, the result part of chapter 2 will focus on the lethal phenotype observed during embryogenesis in absence of Oct-1 and gives an overview of the possible role of Oct-1 during mouse embryonic development. We showed that the embryos die around 8 dpc due to an arrest of the ectoplacental cone and giant trophoblastic cells development which occurs at 6.5dpc. This extraembryonic deletion leads to the formation of an impaired mesoderm.   In introduction the chapter 2 gives a general background about the different developmental embryonic stages in mouse and describes in more details the gastrulation and the different pathways and factors associated.  

The versatile transcription factor Oct-1 : a crucial protein in embryonic development and a key component of the stress cellular response

De Winkel, K.N.

Correia Gracio, B.J.

Knowledge of human motion perception can be applied in the optimization of motion cueing algorithms. In the past it has been shown that some discrepancies between the amplitude or phase of a visual and inertial cue go unnoticed. These acceptable discrepancies are referred to as coherence zones. In the present experiment we investigate whether a coherence zone applies to the direction of visual and inertial motion cues. More specifically, we investigated how much heading of an inertial stimulus may deviate from a visual stimulus suggesting ‘straight ahead’ motion, before the ‘straight ahead’ percept falls apart. Subjects were presented with congruent visual-inertial linear horizontal motion stimuli with varying heading and incongruent visual-inertial linear horizontal motion stimuli, in which a visual cue suggesting straight ahead motion was coupled with an inertial heading cue with varying heading. Subjects judged I) whether or not they moved straight ahead, and II) whether or not the visual and inertial stimulus were congruent. We fitted psychometric curves to the combined judgments and calculated detection thresholds for a violation of either criterion. The results show that the 50% detection thresholds are larger in the incongruent than in the congruent condition. We interpret the threshold for the incongruent condition as the size of the coherence zone. In conclusion: we provide evidence of a coherence zone for heading, as wella as a measure of the size of the heading coherence zone.Control & OperationsAerospace Engineerin

The versatile transcription factor Oct-1 : a crucial protein in embryonic development and a key component of the stress cellular response

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